








key: cord-272179-wvw5mmy3
authors: Calderaro, Adriana; De Conto, Flora; Buttrini, Mirko; Piccolo, Giovanna; Montecchini, Sara; Maccari, Clara; Martinelli, Monica; Di Maio, Alan; Ferraglia, Francesca; Pinardi, Federica; Montagna, Paolo; Arcangeletti, Maria Cristina; Chezzi, Carlo
title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy
date: 2020-10-02
journal: Int J Infect Dis
DOI: 10.1016/j.ijid.2020.09.1473
sha: 
doc_id: 272179
cord_uid: wvw5mmy3

OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. RESULTS: 474 samples (52.3%) were positive for at least one virus for a total of 583 viruses detected. Single infections were detected in 380 (80.2%) samples and mixed infections were detected in 94 (19.8%). RSV (138/583: 23.7%) and RV (130/583: 22.3%) were the most common viruses identified, followed by SARS-CoV2 (82/583: 14.1%). RSV predominates until February with 129 detections and drastically decreases in March to 9 detections. SARS-CoV-2 absent in our area until February 26, in just over a month reached 82 detections. SARS-CoV-2 was found in mixed infections only in 3 cases all observed in children younger than one year old. CONCLUSIONS: This study showed a completely different trend between SARS-CoV-2 and the "common" respiratory viruses that have seen children most affected without distinction of sex, as opposed to SARS-CoV-2 that have seen adult males the most infected.

Viral infections of the upper and lower respiratory tracts are among the most common illness in humans, mainly in children and infants in whom the infection can occur 5 to 6

times for year (Berry et al, 2015) . Briefly, the nucleic acid was extracted from 200 µl of specimens by using the NucliSENS® easyMAG TM extraction assay (BioMérieux, France). The nucleic acid amplification was carried out on the Applied Biosystems 7500 Fast DX thermalcycler (Applied Biosystems, USA) at 25°C for 2 minutes for UNG incubation, and then at 50°C for 15 minutes for the reverse transcription step, followed by the enzyme activation step at 95°C for 2 minutes.

Then, the amplification was carried out for 45 cycles (3 seconds at 95°C and 30 seconds at 55°C).

In the prospective analysis, a specimen was considered negative for SARS-CoV-2 if markers N1 and N3 cycle threshold growth curves do not cross the threshold and the RNase P growth curve cross the line. Conversely, if markers cycle threshold growth curve crosses the threshold line, the specimen was considered positive for SARS-CoV-2 virus.

In the retrospective analysis, only N1 marker was used. Table 1 ). The distribution of single and mixed infections on the basis of age and sex is shown in Figure   1A and 1B, respectively. Overall, a total of 583 viruses were detected, RSV (138/583: (Table 1) .

Similarly, the 60.5% (347 out of 574) and the 14.5% (48 out of 332) of the children and adults tested, respectively, were positive (p <0.00001; OR: 9.04) for at least one respiratory virus other than SARS-CoV-2; for this virus the 1.4% (7 out of 513) and the 24% (75 out of 313) of the children and adults tested, respectively, were positive (p <0.00001; OR: 0.04) ( Table 1) . Table 2 (Berry et al, 2015) . This suggests that many respiratory pathogens may remain undetected.

All novel emergent respiratory viruses have varying but significant impact on human health and the potential to give outbreaks (Berry et al, 2015) ; SARS-CoV-2 as seen in these months, has shown, worldwide, its own unique potential to give epidemics.

In this study, we investigated the viral etiology of ARIs in 906 patients with acute respiratory tract infections, both outpatients and inpatients, attending the tertiary care 

The samples analysed in this study were sent to the University Hospital of Parma for routine diagnostic purposes, and the laboratory diagnosis results were reported in the medical records of the patients as answer to a clinical suspicion; ethical approval at the University Hospital of Parma is required only in cases in which the clinical samples are to be used for applications other than diagnosis.

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. 

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